Shinobi Hero
by NarutoDimensions
Summary: The people call him Shinobi or Ninja and he is the hero of New York. Or he used to be until he joined a team of other young heroes on covert missons under the guidance of the Justice Leauge. Now instead of protecting a city, he is protecting the world.
1. Epilouge

Disclaimer: I Do Not Own Naruto Or Young Justice

* * *

XxX

 **Unknown**  
 **2008 January 4, 21:32 EDT**

"Doctor Desmond, how is the weapon coming along?"

Standing before the gathered leading council of the newly formed Light, the Head of Cadmus wrung his hands nervously as he was stared down by what he could only assume were the scariest people on Earth.

"He is still growing but the Gnomes are working to perfection and there have been no complications. The weapon should be ready in two weeks' time."

"And you're new, _partner_?" L-4 questioned distastefully.

Desmond flinched at the mere mention of the man the Light had stationed at his lab in DC. "He is very helpful in regards to the science. But something is not right about him. He's-"

"As long as he does his work we don't care," L1 said and the half crescent of screens went black leaving him in the dark.

"What am I, Doctor Desmond?"

Desmond flinched as his partnered slithered out from the shadows with a grin on his face.

"Oh, we would have so much fun together. But that will have to wait."

* * *

XxX

 **Washington DC**  
 **2008 January 18, 19:19 EDT**

 _His life was like a movie. That would have been the best way to describe it. Not like he was living in a movie where everything went according to plan and there were enough happy endings to even out the horrible world they lived in but more like he was watching a movie about the life he had lived. He could remember and see what happened but the emotions that went along with the memories were...absent._

 _He saw his brother in all but blood betray and nearly kill him, yet he didn't feel sad or angry, he just didn't care._

 _He remembered receiving news of his godfather's death and watched himself mourn but the sadness and grief alluded him._

 _He watched as an entire world went to war against a madman and then a false goddess and almost win before everything went wrong and he was booted from his dimension into a new one. Watched as those freaks in white jackets found him and brought him here where he died._

 _Yes, died. It shouldn't have been possible for him to have remembered taking his last breath but he did. And it was one of his first memories. He had no idea how they brought him back to life but he didn't question it. He should have but the little devil on his shoulder told him to let it go and he listened._

 _The next seventeen years had passed in a blur of fighting, stealing and killing for the people who had saved him, or so he thought._

 _For the past few months, ever since the little guy who always occupied his shoulder fell off for a few minutes during a fight he had been having second thoughts. When he had brought it up to a doctor he had been sedated and heard someone order him to be put back in his pod for reconditioning. That was what had shocked him out of his mindless drone mentality as the guards attempted to escort him back to whatever machine they had used to control his mind. What followed was a slaughter as he escaped the compound he had called home for his entire life. Non-stop Blood, fire, and bullets for what felt like hours before he felt the sun on his face and just started to run. He didn't know where he was going or what came next but being someone's puppet was behind him._

Line

Watching the mayhem unfold from his fortified Office Desmond slammed a fist against the top of his desk looking away from the security footage to glare at the man standing next to him.

"What is the meaning of this?" He demanded his anger clouding his judgment. He had momentarily forgotten that his _partner_ could kill him in the blink of an eye. "Are you not going to go after him? You can't let him get away!"

His partner shook his head a sick grin on his face. "I'm only a scientist. Capturing run away's is Guardian's job."

"He cannot be allowed to leave!" Desmond was near hysterics. "Do you understand the consequences we will suffer for losing him?"

"I can imagine the consequences _you_ will suffer. As for me, I'll be gone before they find out what's happened."

Desmond gasped as a sickly white hand wrapped around his throat.

"Please give the Light a message for me, Desmond." The hand began to squeeze slowly cutting the doctor's air supply. "Let them know that I thank them for all of their help, and that the game has just begun. Kukuku."

* * *

XxX

 **Bludhaven**  
 **2008 March 4th, 22:47**

Sitting on top of a Wayne Tech building dressed in black pants and a jacket with the hood drawn up Naruto Uzumaki stared down at the black van pulling up to the security gate. He had gotten an anonymous tip that the building was going to be robbed tonight so he was watching anything that moved below like a hawk. Usually, he didn't look into tips sent in without evidence but Wayne tech had too much technology that could be altered to cause mass destruction so here he was in the middle of the night waiting for something to happen.

He didn't like it when there was nothing for him to do. The silence gave him time to think and thinking always led back to replaying the missions he had done for Cadmus over and over in his head. Six months had passed since he had escaped and while without the Gnome constantly controlling his thoughts his mind was free influence it was also lacking the barriers the Gnome constructed to hold back his less than stellar memories. All the experiment's and procedure's he had endured. The constant poking and prodding of needles digging into his skin injecting him with whatever concoction the scientist had created.

But even after he had escaped from the cloning facility they still had a hold on him. In his mind which was arguably more dangerous than physically being with them.

"Hey! Stop right there!"

Turning in the direction he had heard the shout come from Naruto saw a garbage truck filled to the brim with an SUV following behind it speeding towards the west security gate. Leaning forward he channeled Chakra to his feet sticking himself to the side of the building as he ran straight down.

 _"It's a battering ram!"_ The thought struck him as he was halfway down the building but there was no way to contact the guards.

Watching stoically as the suicide driver plowed into the reinforced guard post and exploding killing everyone inside the vehicle and the three guards he kept running trying to reach the ground before the SUV made it into the building's garage.

Dropping the last two stories he cushioned his landing as much as possible with his chakra he hit the top of the Suv feet first caving in the roof. Crouching down low practically hugging the roof of the car ducking the ceiling as they crossed into the underground garage. Rolling off the roof as the driver hit the brakes he grunted as he hit the ground.

Using his hands to spring himself back to his feet he charged the Suv as the passenger door swung open. Kicking it closed as a thug got half way out he ignored the loud crack of a leg snapping and the scream of pain afterward.

Vaulting over the hood he slid to the ground ducking underneath the barrel of a rifle as it started spitting bullets. Rising up he grabbed the gunners hand and forced the gun to the roof. As the magazine emptied he yanked it and the top half of the thug's body back down bringing his knee up to meet him halfway.

 _"Only two?"_ He thought letting the unconscious criminal fall to the floor and checking the inside of the van. These two idiots were breaking into one of Wayne's building's with two guys and two guns? That didn't make sense.

Walking around the car he grabbed the last thug by his collar and dragged him from the car slamming him against the side of the Suv. "Why are you here? Are there others?"

"Why are you here? Are there others?" He demanded.

"I'm not telling you-"

Across the parking garage, the elevator doors slid open and Naruto ducked behind the car dragging his captive with him keeping a hand over his mouth.

"Where are those idiots?"

Narrowing his eyes at the grey masked man leading a group of three others who were pulling large crates behind them Naruto frowned. Sportsmaster had gotten into the building without setting off one alarm. Wayne Enterprises had some of the best security defenses in the world. Sportsmaster was good but he wasn't that good.

Slamming the thugs head against the ground he moved around the car and grabbed assault rifle laying on the ground.

He couldn't kill the criminals. As much as he wanted to he knew the Justice League would stop him even if he was doing good. But that didn't mean he had to take it easy on them. When they went to jail they would want to stay there out of fear of what he would do to them if they escaped.

"Over there, boss." One of Sportsmasters cronies said pointing to the corner where the van was stopped.

Setting up his sights Naruto took the man's knees out with two bullets and did the same for the other two four more. Sportsmaster who was positioned behind the crates ducked down out of the line of fire.

Growling he kept his gun on his shoulder and started moving forward using the cars of Wayne's 24/7 work crew for cover.

Moving through the lot he stopped to cars from the crates and waited for five minutes to see if Sportsmaster was going to make a move. When he didn't he moved again making a wide half-circle keeping ten yards between him and Sportsmaster. He was the one with the gun. No need to get close.

 _"He's gone."_

Behind the crates was nothing but air. Sportsmaster had gotten away.

"Hey, don't move!"

Now they show up. Naruto tossed his gun to the ground and raised his hand as five security guards came out of the elevator side arms trained on him. Rolling his eyes as the guards came towards him he fingered the hidden blade in his sleeve. Drawing it, with a quick nearly untraceable flick of his wrist he sent it flying into the lights on the ceiling.

"Where'd he go?"

"Do you see him?"

Silently slipping out of the parking lot Naruto left the guards and the thugs behind vanishing into the night.

* * *

XxX

 **In Orbit, Watchtower**  
 **2008 March 5th, 03:39 EDT**

 _"Who are you?"_ Sitting in front of the main computer on the Watchtower, Batman watched as the hood figure took down Sportsmasters team of hired thugs who were trying to steal from the Wayne Enterprises Bludhaven branch building.

He was military trained. Bruce could see that from just watching the way he ambushed and shot the would-be thieves before closing in on Sportsmaster who had fled. The problem with that conclusion was that from the shape and height, the hooded figure was in his late teens. He doubted he had even reached adulthood given his size. And those answers only led to more questions.

Where did he come from? Why was he at Wayne Enterprises? What was he after? Who trained him?

"Zatara to Batman, requesting full league response."

Shutting down the video he sent the file to the Bat cave and headed for the towers Zeta tube. The League needed his help now, but he wasn't letting this matter drop.

 _'Who are you?"_

* * *

 **A reboot of the original story.**

 **Hope you guys like this one as much as the last!**

 **Thanks for reading and leave a review with pairing and what you think so far!**


	2. Chapter 2

Disclaimer: I Do Not Own Naruto or Young Justice

* * *

 **XxX**

 **Metropolis**  
 **2008 August 14th, 20:15 EDT**

"Sir, last of the crates are loaded up and we are ready to move."

Standing before his gathered army made up of the Black Hawk protection agency Naruto smiled politely at Mr. Gaynor. The man in charge of Black Hawk.

"Then we should get moving. I don't like being in Metropolis. Too much collateral damage."

"So, you're moving to Bludhaven? That place has more crime than Metropolis." Gaynor said escorting Naruto to the limousine waiting in front of the convoy of Semi-trucks lined up on the road.

Naruto nodded in agreement sliding into the back of the car Gaynor following after him looking completely out of place in full tactical gear.

"Maybe so," He said looking over his shoulder at the LexCorp warehouse slowly disappearing from view. "But it's human crime. I can hire guards with guns to protect me and my interest from thugs with I can't pay for is a way to stop my building from being destroyed by super-powered aliens.'

Leaning back in his chair Naruto closed his eyes and ignored the feeling of being stared at. It had been a constant thing since he had hired Gaynor to protect _"his"_ cargo. He knew that Gaynor was suspicious and that while his trust fund brat moving his more expensive items was a decent cover it wasn't full proof. Luckily though a rather generous donation from the crime families in Bludhaven and Lex, he was able to put enough zeroes behind the check to keep any questions from being asked.

Explaining to Gaynor that he wasn't a millionaire and that his agency was really helping him steal millions of dollars of equipment from a Luthor Corp black site wasn't on his to-do list.

Not that it would have mattered if they knew anyway. No one working for him saw who he really was. All they saw was his Henge, the mid-twenties, dark-haired, brown-eyed CEO of Whirlpool Industries. A newly formed company run by the young Millionaire Sarutobi Hiruzen, who came from a family with old money and decided to not waste it away on cars and expensive clothes.

And given that the places he had been hitting weren't registered to LexCorp or any of its subsidiary's Lex couldn't file a report. All his old handler could do was stew knowing that everything he had created to combat the heroes of the world would now be used by one.

Not a well-known one, but he would be soon.

* * *

 **XxX**

 **Bludhaven**  
 **2008 September 20th, 22:48 EDT**

 _"It's time."_

Standing in his secret base Naruto watched as the footage of a group of thugs took down a FEMA truck on route to deliver medicine to hospitals in the Narrows played on the holographic screens in front of him.

The Narrows was the worst part of the already corrupt city. Not even police, corrupt or not went there unless forced and if they did they kept to themselves in fear of their lives. Criminals had been running free for so long he doubted they even knew there were consequences for their actions anymore. But tonight that changed. He wouldn't be able to fix the city overnight or even just a part of it like the Narrows. However, fear was a strong motivator and Bludhaven's underworld was going to learn to fear him tonight.

Shutting the screens down with the holographic computer mounted on his wrist and forearm he activated the camouflage of the room and stepped back as the screens vanished, the walls spun and the floor moved.

Around him, the room morphed from high-tech lab to an apartment flat with sofa's bookcases and collectibles. As well as the clock window opening giving him a view of the city. ( **Clock tower from Arkham Knight)**

Pulling his grapple gun from his belt he aimed at the roof firing as the hidden door opened letting moonlight shine into the tower. Gripping the gun tight he tensed as the hook set and began to reel rapidly dragging him into the air.

Flying out the trap door and a good ten feet into the air before falling back down to the roof he channeled chakra into his legs and began running across rooftops clearing the street wide gaps with ease heading for the Narrows.

As he moved his enhanced hearing caught the frantic voice of a woman yelling.

"Let go!"

Changing course he jumped to the other side of the street landing on the roof of an old diner. Moving across the roof he peered over the edge into the alley behind it and saw four men cornering a young woman in a waitress outfit. They had formed a half circle and pushed her against the wall laughing as she cowered.

"Tonight's are lucky night boys." One of the men said reaching for the girl.

On the roof, Naruto smirked behind his helmet. "No, it isn't."

Drawing a pair of throwing knives from his utility belt he threw them at the man who was talking.

Not wasting any time he jumped down into the alley landing behind the three men still standing as their leader folded in on himself crying and shouting all while grasping at his crotch. Exactly where he had been aiming.

"Who the hell is this guy?" One thug asked drawing a knife from his boot.

The other two also drew knives and the three began moving towards him leaving the fourth on the ground.

 _"So much for loyalty."_ Naruto thought as a thug lunged forward stabbing at him. Faster than either the thugs or the waitress could see his hand lashed out wrapping itself around the thug's wrist and twisting viciously until he heard a loud crack.

"Ah!"

Ignoring the goons screams he kept his hold on the man's wrist and turned the arm until the forearm was facing up before jerking it again, this time towards the sky snapping the bone at the elbow. Still holding on he kicked a foot out catching the now crying man in the knee sending him to the ground with another broken bone before shoving downwards forcing the arm he was holding out of its socket before letting go and stepping back.

"What's going on out here? Caitlin?" The lights in the alley flicked on and the two remaining thugs got a good view of what they were up against instead of the shadowed silhouette they saw before.

"What the hell," one whispered taking a step back.

Naruto activated the LED's in his helmet on and the eyes of mask glowed an eerie blue. Looking over the thug's shoulder he looked at the waitress who flinched at being the focus of attention again. "Go back inside."

"Go back inside."

Caitlin nodded hurriedly and ran to the back door where a stocky chef was waiting for her wielding a butcher's knife. When she got there the chef let her inside and shut the door.

Hearing the lock on the door click Naruto turned his attention back to the thugs drawing another throwing knife from his belt.

"Thousands of years ago, before society had sympathy for their criminals a thief's hand would be cut off as punishment. To stop him from doing it again." Naruto waved the knife at the first thug he had taken out. "I have no sympathy for criminals."

The thugs flinched as his robotic warbling voice echoed in the night.

* * *

XxX

In Orbit, Watchtower  
2008, October 4th 20:10 EDT

Gathered together in the main conference room aboard the Watchtower, each member of the Justice League had their attention concentrated on the screens in front of them.

"This is...um," Green Arrow cleared his throat awkwardly not sure how to start the conversation while simultaneously worried about breaking the silence of the room. He could see some of the other Leaguers weren't sure how to respond either.

"Should we do something?" He finally asked after another minute of silence.

Superman who had looked away from his screen was the first to speak. "Of course we should do something! We can't let this maniac run around any longer."

"Why?" Wonder Woman glanced up from her screen. While not ideal she did not understand Clark's vehement reaction. "He is making his city a safer place. Just as we do-"

"No," Superman cut her off slicing a hand through the air in front of him. "Whoever this is, he is not like us at all and we are not like him. This is not okay."

Most of the League nodded in agreement shutting their screens off. No longer wishing to look at the photo being displayed. A single camera shot of a man handcuffed and hanging from a light pole in Bludhaven. He wasn't dead as his terrified eyes were locked onto the camera but he wasn't in the best shape. His face was bruised and bleeding, one leg was twisted at an awkward angle and there was a knife stuck right below his waist.

"I do not understand. This man was a criminal." Wonder Woman frowned. Why was Clark defending someone who would do such a horrid act?

"Yes, but they are also human," Superman argued. "I do not condone what he did or tried to do, but he should face justice for his crimes. Not be tortured. Can any of you condone this?"

Clark looked around the room at each member of the League before landing on Batman who sat opposite to him. Easily the most brutal of the League members his stance on the subject would count for more than the other. It would either show them that what was happening in Bludhaven was unacceptable even by the Dark Knight's standard or it would give those who agreed to let it go a well-respected member to stand behind.

"Do you?"

"No," Bruce answered immediately already having made up his mind on the subject. His answer shocked more than a few members as they were expecting something else but he continued putting that shock to rest. "But given the alternative. I will accept it."

"Batman, you can't be serious?"

"We will put it to a vote," Batman said. "Anyone who wishes to pursue Bludhaven's _"Bloody Knight"_ hands up."

Waiting and counting as more hands followed Superman's example Batman nodded once the voting was done. It was close but ended as he predicted. "Then it's settled. For now, we stay out of Bludhaven. No one is to make contact with the Knight until we know more about him."

* * *

XxX

 **Bludhaven**  
 **2008 December 25th, 21:17 EDT**

 _Tobias church._ A ruthless crime lord who will stop at nothing in order to get what he wants. Rumored to have conquered the crime in Hub City by murdering the crime lords in it to create one gang under his rule.

 _"And given gang wars have all but stopped I'm inclined to believe it."_ Naruto thought as the helicopter carrying the crime lord drew closer to the building he was on. Out in the open in his full knight gear, he waited for the helicopter to land. He could have hidden in the shadows, turned off the LED his helmet and got the jump on Church but he wanted the man to know what was coming when he landed in Bludhaven. Give him the chance to turn around.

Not that he would have actually let the criminal get away. No, Church was too dangerous for that but with a rumor that even the man who ran half of Bludhaven's underground wouldn't step foot in the city while he was patrolling the streets circling around the fear he put in criminals hearts would grow.

So he stood and he waited as the helicopter landed and the side doors slid open.

"Luthor?" He hissed as instead of the crime lord and even worse man stepped out onto the roof.

Dressed in a thousand dollar suit, smirk on his face Lex strode away from his ride and towards his former pawn ignoring the whipping of his tie in the wind.

"Naruto, I see you're making use of my stolen goods."

"Stolen?" Naruto asked. "I didn't hear anything on the news about LexCorp being robbed."

Lex fixed his tie once he was out of the winds, patting the black cloth down against his white shirt. "You know that is not what I was talking about, Naruto. Do not play the fool, we both know you're not one. I did raise you after all."

"I wouldn't call keeping me in a cage when not on missions and implanting knowledge with Gnomes _raising_ me. But to each his own, right?"

Naruto could tell he had gotten under Lex's skin with his acquirement of LexCorp's grayer prototypes. It didn't show on the CEO's face but nothing ever did unless it was part of an act. Lex always wore a mask, always pushing what he really felt down and holding it inside as he played the role required of him. _"It's probably why he's insane."_

"Why did you pretend to be Tobias Church?" He asked pushing past his thoughts of the CEO. Maybe once upon a time, he had cared that Lex was driving himself more and more insane but those days had passed now. He knew the truth. And the truth was Lex had been gone for years. What he had to focus on now was his city.

"I knew you would come running," Lex smirked. "Since I don't know where you're little secret hideout is I needed you to come to me and this was the easiest way. You're very predictable. Probably thought you would show up here scare or beat Tobias and then the criminals here would fear you even more. Am I right?"

Naruto bit his tongue underneath his helmet.

"Of course I'm right. Because we've spent years together. I know you better than you know yourself. It's how I know your little crusade isn't for the good of others. It's for you and you alone. To atone for everything you've done for Cadmus, right? Wipe away some of the blood on your hands."

Lex's smirk widened as Naruto's hands clenched. "Tell me, Naruto have you even thought of anything other than cleaning up Bludhaven the past year? Or have you just been pushing it all away? Your past? Who you really are? _What_ you are?" It's-"

"Enough!" Naruto cut the CEO off. He didn't want to hear another word. Lex didn't know what he was talking about. "What do you want, Lex?"

"Nothing, I was just passing by and thought I'd stop in." Lex turned around and started walking back to his helicopter.

Naruto watched him go wishing there was a way he could stop him but knowing there wasn't'. Lex had been able to knock back any accusation the League or anyone else had thrown at him for years. And it wasn't like he could just grab the CEO and throw him in a black site. A man of Luthor status would have half the country looking for him.

No, all he could do was stand by and glare at the smug smirk that said 'you can't touch me.'

As the door to the helicopter slid open again Naruto frowned as something tickled the back of his mind. Looking away from Luthor he stared at the man holding the door open. He sensed something emanating from the man. Like a power source.

The man as wearing a black balaclava that hid his face but the grey Gnome on his shoulder was in plain view and Naruto saw its eyes glow.

 **"Go to Bialya. Naruto."** A foreign voice said in his head.

 _"Who are you?"_ Naruto demanded through the link the Gnome established. _"Why Should I go to Bialya?"_

 **"You escaped, others have not. You must go to Bialya."** the voice said again.

 _"Who are you? I won't go unless you tell me your name."_ Naruto said resolutely. He had always known his wasn't the only life Cadmus had ruined but the locations of other labs were always kept secret. And now he was just being given the location of one after Luthor shows up. It was a trap. It had to be.

The voice spoke again as the helicopter rose into the air. **"I am Dubbilex, a Genomorph who wishes for freedom for my brothers."**

Naruto frowned as the presence in his mind vanished. He needed to get back to the clock tower and start looking into Bialya. He didn't trust whoever this Dubbilex was but if there was even a one percent chance that other clones like him were being held there against their will he had to treat it as an absolute.

* * *

 **Thanks for reading and leave a review with pairing and what you think so far!**


	3. Chapter 3

Disclaimer: I Do Not Own Naruto Or Young Justice

* * *

XxX

 **Gotham**  
 **2009 January 6th, 20:18**

Walking through Wayne manor silver tray in hand Alfred sighed as he set the tray down on top of the piano in Master Bruce's study and played a little tune. Behind the piano, the books shifted sliding away from each other revealing the hidden elevator behind them.

Picking the tray back up he entered the secret room and typed in the passcode that would take him down. The elevator doors closed encasing him in complete darkness for half a minute before they opened again.

Stepping out on the metal platform the old butler frowned. "Master Bruce, you forgot dinner...again."

"Something came up, Alfred," Bruce said not looking away from the many screens of the bat-computer.

Sighing Alfred set the tray down and didn't bother removing the lid knowing it wasn't going to be eaten tonight. "What is all this?"

"The Knight in Bludhaven."

"Ah, yes. The new hero that has your co-works split down the middle. What about him?"

"Nothing yet. And that's the problem." Bruce growled as his fingers flew over the keyboard typing in commands. "Look."

Backing away as the three large holographic screens were broadcasted from the bat computer Alfred and Bruce looked over the image. Bruce with suspicions and Alfred with worry.

"These are-"

"The finished product of three of LexCorp's prototypes." Bruce nodded tapping on screen enlarging the image. "The 8.03 armored suit. It's an advanced suit designed with flexible plates overlaying an MR-fluid (magnetorheological fluid) armor layer and incorporating the latest in cutting-edge technology. The tri-weave bodysuit consists of an outer and inner layer made from a titanium-dipped tri-weave fiber mesh. Sandwiched in between is the MR-fluid based liquid armor system. MR-fluid hardens in response to impacts, specifically designed to provide superior shock absorption, as well as enabling greater force delivery behind counterattacks. The liquid body armor layer is also more flexible than the ceramic or fiber-based alternatives used in previous suits, allowing for greater maneuverability." **(Arkham Knight Suit)**

Alfred glanced between the picture of the Bludhaven Knight and Gotham's Dark Knight. "Isn't your suit made of the same thing?"

"Yes, Wayne Enterprises is currently working on a way to make suits like it cost affordable or the military." Bruce closed the image down and enlarged the second. "Then there is this-"

A black car that looked more like a tank was displayed and Alfred gasped. "Oh, my."

Bruce nodded to the reaction. "A Wayne Tech prototype armored tank designed as a bridging vehicle for the military. How Luthor got his hands on the schematics I don't know. There seems to be a few changes but from what I can see those were done by the Knight and not LexCorp." **(Dark Knight Tumbler)**

"And what is this?" Alfred questioned tapping the last screen.

Bruce frowned. "That is a prototype stealth aircraft. All I know so far about it is it can move at supersonic speeds and has advanced stealth systems." **(Arkham Knight Batwing)**

"And you know this how?"

"Two hours ago the Watchtower radar caught it leaving Bludhaven before it vanished." Bruce pointed to a screen displaying Middle Eastern countries. "I picked it up again one hundred miles from Bialya's border."

"That is quite a ways away from Bludhaven." Alfred stepped back as Bruce went back to work on the bat computer. "Do you know what he was doing?"

"I can't be sure but one hour ago there was a massive underground explosion. Queen Bee covered it up but something happened. And the Knight was involved somehow. It's no coincidence that it happened only hours after he arrived in the country. I need to know what he was doing in Bialya."

Of course sir." Alfred sighed worriedly. He had seen when Bruce became so fixated on something it consumed him. And it was never easy to deal with. For him or Master Richard.

Bruce turned his full attention back to the screens. Something was going on he just needed to find it. Typing in another command he hacked LexCorp's servers and connected the alarms to the bat computer. If another break-in happened he would know.

* * *

XxX

 **Washington DC**  
 **2009, March 8th 13:00 EDT**

"Doctor, why does it seem as if every time we speak you only have bad news?" Lex asked as he was led through the primary Cadmus lab in DC. Desmond had contacted the Light again to report another experiment or asset going rouge. The others members had finally had enough and despite the possible gains, he would concede that right now it just wasn't worth it anymore.

"Sir, I do not think this course of action is the best. Yes, there have been minor problems but we can't -"

"We can and we will." Lex cut Doctor Desmond off. He and the Light were tired of the man's failures. "Three of our best operatives have gone rogue, doctor. The first we could understand. He had always been unstable, but there is always a price to pay for power and the Light deemed it acceptable. However, second-generation operatives escaping is unacceptable. They do not have the power of a first generation, why should we pay the same price?"

Desmond stayed silent. How was he supposed to argue when Mr. Luthor was correct. They had assumed due to the nature of the first generations physiology it was why none of them could be controlled absolutely. It was fifty-fifty with every operative on whether they would need to be put down or could be kept operational. After nearly the entire program had been wiped out and the low birth rate they had scrapped it and focused on Generation two, which was now showing problems as well. But he still couldn't let them destroy everything.

 _"Dubbilex, has he been moved?"_

 **"Yes, doctor."**

Lex stopped as they reached the doctor's office.

"Mr. Luthor?" Desmond asked cutting his mental link to Dubbilex.

"You keep your door locked at all times, do you not?"

The brown haired doctor nodded. "Of course, my work is very sensitive."

Lex stepped away from the door and pressed the small panic button disguised as a button on his cuff.

Desmond moved back as well as finally noticing that the door was not closed all the way. Too caught up in his plans against the Light to see the small gap. If Mr. Luthor hadn't been with him he could have just been assassinated.

Watching Desmond from the corner of his eye Lex saw the scientist breaths start growing deep and frowned. Now was not the time to panic. Someone had infiltrated Cadmus main headquarters. No one but members of Cadmus and the Light were supposed to know that the building had more than two stories. So how did someone not only get in but get down to the lower levels?"

"You can come in, Doctor, Lex. I won't bite." A young but familiar voice called from inside the room.

Lex and Desmond looked at each other. The voice was one they had heard for years. The problem was they didn't know if it was still on their side or not.

Choosing not to show fear Lex walked forward and pushed the door open stepping into the office. "Naruto, how good to see you."

Seated behind a polished oak desk a blonde teenager had boots kicked up on the table and was flipping through a manila folder. "You know, Lex, I knew you were resourceful, but _how the hell_ did you get ahold of Superman's blood? And enough to clone him?"

Naruto whistled his boots off the table grinning at the billionaire CEO. "I'd say you had some serious stones for pulling something like this off but we all know Supes not going to do anything. But still, how you do it?"

"You're one of the rouges," Lex stated more than asked as he sat down in the chair in front of the desk. "Why are you here?"

"Do you even know which one I am?" Naruto asked casually as he grabbed another folder. "I doubt you do, not that I really care but I had to ask."

"No, I don't know which clone you are. You all look the same after all."

Naruto smirked and ran a hand through his short cut hair. "We used to you mean. Anyway, I'm here because I wanted to offer my services to Cadmus."

"Your services?"

"Yea, you see, the past two months, ever since I rabbited, I've been working as a mercenary," Naruto admitted without shame. Sure it wasn't the most morally ambiguous career but that was in this world. Naruto prime as he liked to call his original was from a world of mercenaries. Really, all he was doing was going back to his roots. No one could fault him for that, right?

"The problem is I'm not very well known in the community and well," Naruto motioned to himself. "I'm only fifteen, who's going to take me seriously? Unless a well-respected criminal hired me for a job. Someone like you. If word got around at even the mighty Lex Luthor hired me I would get more business."

Lex didn't answer immediately. He was slightly stunned by the gall the clone before him had. To break back into Cadmus then ask for a job after betraying them. It was ludicrous but there he was sitting behind Desmond's desk smiling smugly like he had accomplished something. "The arrogance."

"And what is stopping me from having a squad of G-Trolls throw you in a cell? Because rest assured I will not pay something I created to work for me."

Naruto met Lex glare with a smile and reached into his jacket pocket. Lex had been arrogant. It was why he believed that he could take a being from another dimension with strange powers and clone a private army from his blood. That same arrogance also pushed him to create a second generation without the powers when his first army turned on him and each other.

It was also what made him comfortable enough to threaten a person who had shown they could infiltrate his highly classified building. He would have to teach the CEO a lesson in humility.

Pulling his hand from his jacket he shook it and smiled at the minuscule tensing in Lex's. "I'm guessing you already know where I'm going with this but I'm going to tell you anyway. Hidden on each level are bombs that will go off if I press this button."

Naruto ran his thumb over the red button on his detonator.

"And then boom!" He whispered walking past Lex and out the door. "If you ever change your mind I'm sure you'll figure out a way to contact me."

* * *

XxX

North Rhelasia  
2009 June 19th, 21:36 RLT

Naruto stared down through the grate in the vent he was hiding in, watching as Singh Manh Li, the leader of North Rhelasia worked. This was his third job since rumor had gotten out that he had managed to break into a LexCorp building and confront the man in charge himself. Luthor was known widely as one of the most paranoid people in the U.S and his security only proved that point.

And since Lex upped that security to an even higher level on his more _"sensitive"_ buildings right after the rumor began swirling around, rumor became truth and his encrypted phone started ringing.

That was how he found himself in the North spying for the South. Truth be told he had expected the South to want him to steal classified document or assassinate Singh, not that he would have accepted a mission like that. In the heat of the moment or a really terrible person, he didn't mind getting his hands blooding but killing a foreign countries leader would attract too much attention. League Attention. And that just wasn't worth it, no matter how much he was getting paid. At least not until he had a way to defeat each League member.

For now, he would stay off the Leagues radar. Money wouldn't do him any good if he was sent to prison where he couldn't spend it.

* * *

 **Thanks for reading and leave a review with pairing and what you think so far!**


	4. Chapter 4

Disclaimer: I Do Not Own Naruto Or Young Justice

* * *

XxX

 **Washington DC**  
 **2010 July 5th, 00:08 EDT**

 _"Activate every Genomorph in Cadmus."_

Above where the fighting was going on in the lower levels of Cadmus two blue eyes opened. Beside them, another pair of eyes glowed bright red.

 _"Capture Robin, Kid Flash, Aqualad, and the weapon. They must not be allowed to escape."_

Punching through the film holding him in his pod a blonde haired teenager stepped out barefoot and shirtless wearing nothing but a pair of black pants. "I need my gear."

 _"No!"_ The Doctors voice echoed in his head. _"There is no time, just go after them."_

"I would stand a better chance with my-" The G-gnome on his shoulder glowed again and he stopped talking as the genetically engineered telepath on his shoulder taking over his mind.

A second later he started sprinting towards the elevator with thoughts that weren't his own controlling his mind. "They need to be stopped!"

Using his fingertips and enhanced strength he pried open the elevator doors just as the elevator went speeding past nearly taking his arm off.

 _"Level 15 brother."_

Jumping across the gap he fell short of the other side and let himself fall two levels before grabbing ahold of the metal beams on the walls.

"Go left!"

Narrowing his eyes at the four teens running away from him he jumped the gap again landing on his shoulder and rolling into a sprint. They wouldn't get away. Not from him.

"'Um, guys?" Kid Flash said checking over his shoulder. "Who is that?"

The other three teens back as well and saw the blonde guy who looked around Kid Flash's age charging down the hallway after them.

"Don't know but we need to focus on escaping," Robin said as the group followed Superboy's orders and took the next left. They could always come back after they informed the Justice League of what was going on.

"We cannot just leave him here." Aqualad frowned as Superboy called out another order.

"Right!"

That's right. It wasn't right to leave whoever was chasing them in Cadmus' hands. They had rescued Superboy after all.

"We're not leaving him for good. Just until we contact the League and let them know what Cadmus really is." Robin as they rounded the corner right into a dead end.

Kid Flash turned to Superboy. "Great directions, Supey. Are you trying to get us repoded?"

"No, I...I don't understand."

"Don't apologize, this is perfect," Robin explained shoving past Wally to get to the air vent on the wall. "We can get out through here. The air ducts go all the way to above ground."

"Yes, they do. But you four are going down."

The three young heroes and Superboy turned around as the blonde teen chasing them caught up. He didn't look furious anymore, and to their confusion grinned at them.

"Get it? Because the pods are below us, but also because I'm going to take you down. It's wordplay!"

Wally leaned closer to Kaldur. "Is it me or did he seem angrier a minute ago?"

"It is just like with Guardian. He's being controlled by that thing on his shoulder. The Genomorph." Robin pointed out drawing one of his birdarangs. "We don't have time to waste going easy on him. We take him down. Hard."

"Gotcha," Wally smirked racing forwards ahead of his teammates.

Dropping to the ground Naruto laid flat sideways blocking the hallway floor."

"Ah!"

Watching Wally trip over the other clone and tumble down the hallway smacking into the wall Robin and Aqualad shared a glance before charging themselves right after Superboy who was already charging.

Hopping to his feet he ducked a wild right hook from his fellow clone. Grabbing the extended arm he spun putting his back to the Kryptonians chest and leaned forward using Superboy's weight against him throwing him towards Kid Flash who was getting to his feet.

"We are trying to help you," Aqualad said using his Water-bearers to form a mace.

"He is lying. They must not escape Cadmus."

Naruto listened to the voice in his head. It had never steered him wrong before and he didn't know these intruders. Leaning to the right and left each time Aqualad swung the water weapon he back up against the wall and ducked as Aqualad swung again smashing his mace into the wall.

"No!" Aqualad deactivated his Water-Bearers to free his mace as it was stuck in the wall.

Wrapping his hands around the Atlanteans head Naruto pulled down and shoved his knee up slamming it against Aqualads nose sending him stumbling back.

Righting himself Aqualad frowned forming two swords. "Atlanteans skin his very dense."

"Doesn't me I'm going to lose." Naruto shot back grinning a little. It was nice to actually be fighting real opponents instead of the Genomorphs in had strange powers and if they weren't panicking he was sure they'd be a lot harder to beat. And that was exciting.

"You already have."

Naruto spun around ready to counter whatever attack Robin was going to throw at him but was met with two wires and thousands of volts of electricity. Dropping to the floor he hit his knees first then fell flat on his face. "I knew I should have gotten my gear."

Ass his world started growing darker he heard Aqualads voice telling Kr to pick him up.

"Don't give me orders."

* * *

XxX

 **Bludhaven**  
 **2010 July 5th, 04:13**

In the clock tower, blue eyes widened as footage from a Whirlpool Satellite rolled showing the outside of the Main Cadmus branch in Washington DC. The entire Justice League was gathered outside what used to be a building but was now a pile of rubble. Across from them stood three sidekicks that were easily recognizable. Aqualad, Kid Flash, and Robin.

There were two other teens next to them and while curious the boy dressed in white's physical similarities wasn't what was drawing her attention. It was the blonde boy lying on the ground seemingly unconscious.

Behind her, a thud sounded as someone dropped into the room. She didn't need to turn around to know who it was. She had seen him on the security feed.

"You should look at this."

Removing his helmet Naruto leaned over the shoulder of a teenage girl who bore a strikingly similar face to his own. If he wasn't in his early twenties she could have been his daughter but the age gap most would see them as siblings. Which was fine him. No one would believe she was an artificially created clone with implanted memories of multiple doctors if he told them anyway.

"Do you see it?"

"Yes, Naruko, I do. But I thought Cadmus stopped production of clones of me after you and a third went rogue," Naruto asked staring at the clone. Great, now he'd have to talk to the League. And show his face.

Naruko looked up at her boss. "Are you going to-?"

"Yes," Naruto nodded. "If the League sees my face it won't matter. I can show them he's a clone of me."

"And if they don't want to hand a teen over to a maniac as Superman put it?" Naruko knew from the past year working in Bludhaven with her _"father"_ so to speak that he and some of the League didn't get along. They thought he was too harsh on criminals, playing judge, jury, and executioner. Even though he didn't kill. She thought it was dumb. Since he had become an active Hero in Bludhaven crime had dropped dramatically. Criminals were actually terrified of the consequences of doing crime and most were smart enough not to and those that weren't well, they usually didn't do it a second time.

"Oh, hey where are you going?" She asked as Naruto started to walk away.

"The night's not over. There's still work to do."

Naruko shook her head. She doubted he even knew how to take time off.

* * *

XxX

 **Santa Prisca**  
 **2010 June 26th, 00:32 ECT**

Naruto stared at the group of men wearing white and black Lucha libre masks standing in front of him. They were deep in the forests of Santa Prisca and very far from the Venom factory. "Where is Bane?"

He had been contacted by the head Lucha himself to come to the island and now the man sent a bunch of his pawns to do business.

"Bane has been captured by Kobra who has taken over the Venom factory." One of the men said stepping forward as the other six pointed their guns at the young mercenary. "If you help us free him you will be paid."

"Do any of you know why Bane called me here?" Naruto asked as he thought over the offer. On one hand, Bane might not pay him even if he did help rescue him. That would force him to fight the venom user and show that he wasn't someone you could get away with cheating. It would be fun to test his strength against someone like Bane but that would also take away the option of the mission Bane had called him for.

 _"But Kobra would be a good challenge as well."_ He thought. The false god wouldn't go down easy and with a factory full of worshippers the inevitable fight would be fun.

"No," the same guy who spoke before said shaking his head.

Naruto nodded and stuck out his hand. "Alright, I'll help rescue Bane."

The other man reached out to shake it and when he did Naruto squeezed hard. Not enough to break anything but enough to cause discomfort.

"If I do not get paid for this, I will hold you responsible."

* * *

 **Thanks for reading and leave a review with pairing and what you think so far!**

 **P.S to anyone wondering, no, Naruto is not a hero and a mercenary on the side. It is two different clones.**


End file.
